Tuesday, April 24, 2007

Funding UsefulChem

I have talked to a number of people lately about funding sources for UsefulChem. I have also been working with our Institutional Advancement Office at Drexel to contact appropriate foundations. At this point it probably makes sense to put my proposal summary sheet on the blog to get some additional suggestions. Also please forward to anyone who might be interested.

UsefulChem and Open Notebook Science Proposal Summary
contact: Jean-Claude Bradley (bradlejcATdrexel.edu)

The communication of scientific information is undergoing a substantial shift towards openness. There is much discussion about providing Open Access (OA) to journal articles and several publishers are providing an OA option for authors willing to pay for the publication costs. A few publishers are even supporting free access for both authors and readers.

As another step towards a more open system, some forms of open peer review are undergoing experimentation. In one trial, some Nature article submissions were posted for review by the community at large first then submitted for standard peer review. Another longer term and successful open peer review system, ArXiv, has been extensively used mainly by physicists as a pre-print system. Others, like PLoS ONE, are changing the traditional criteria used to evaluate the merit of submitted articles.

However, these examples are still based on the traditional scientific article, a format that evolved within the context of paper based communication. When publication and retrieval costs (time and money) are high, it makes sense to package information as compactly as possible in few larger documents and use relatively few established vehicles. Consider the case of a chemist looking for the prior synthesis of a compound. Before computer assisted searching, finding relevant references was very time consuming and required searching through piles of books at the library. Deciding which references to then pursue was dictated by the availability of the physical document in the library and the likelihood of the information therein being reliable. It made sense to first look for information from a known source that had previously generated quality information and then, only as a last resort, request interlibrary loans or send a card to the author requesting a re-print from sources more difficult to obtain.

In the Google Age, the retrieval and sorting costs for a large number of documents are negligible. Even with pay document databases at university libraries, the costs are generally fixed so that additional searching, within reason, has no incremental additional cost. The reader, who has the most invested in assessing the validity of the work, is really in the best position to act as a reviewer. In the case of a chemistry researcher looking for methods or synthesizing a particular compound, if they are not competent enough to review the merits of the synthesis based on the evidence provided in the paper, they should not be performing the experiment without guidance from a mentor.

Thus, in the Google Age, the most important criterion for the usability of a document is immediate online availability. Articles and information sources that are not immediately available will only be pursued as a second choice, even if the vehicle is reputable.

With the advent of easy to use, free and hosted social software like blogs and wikis, and extremely efficient indexing by major databases such as Google, publication costs and learning curves are essentially zero. It is now possible to connect a researcher providing information with a researcher looking for that information very quickly with minimal technological obstacles.

Keeping the actual laboratory notebook of a research group in real time on a public wiki and holding discussions on a public blog is the natural extension of the openness concept leveraging today's technologies and global infrastructure. Operating with such transparency and demonstrating that science can be accomplished in this type of an environment is at the core of the UsefulChem project.

The UsefulChem project was started in the summer of 2005 by Jean-Claude Bradley, associate professor of chemistry at Drexel University. Initially, the project consisted of a single blog, UsefulChem.blogspot.com, with the objective of carrying out chemistry research in areas that could benefit most from an Open Science model. In a process that was documented in the blog, the synthesis of anti-malarial compounds was identified as a worthwhile objective. Synthetic approaches were discussed and developed, and with new graduate and undergraduate students, lab work was started and recorded online from February 2006. Since then the project evolved to three graduate and three undergraduate students.

One of the graduate students is responsible for developing the automation components of the system. As often repeated by Peter Murray-Rust, a long time champion of Open Science in chemistry, cheminformatics still lags significantly behind bioinformatics, especially when comparing with the quantity and quality of open data in areas such as genomics. By representing molecules, reactions and results in a way that can be universally accessed and understood by machines as well as humans, there is great potential for accelerating progress in chemical research. This is especially true if "failed experiments" are routinely reported since they still provide valuable information to other researchers in designing their next experiments.

With the idea of creating an infrastructure that can be quickly and cheaply duplicated by other researchers, UsefulChem uses free and hosted services like Blogger (blogs), Wikispaces (wikis), YouTube (video), Google Video (video) and ManyEyes (data visualization). However, funding is still needed to purchase chemicals, equipment and support students.

One of the attractive features of funding Open Notebook Science is the built-in transparency of how resources are spent. Just like the rest of the world, a funding source has access to the daily work of the laboratory group and their collaborators and is free to provide feedback at any time.


At 8:04 PM, Blogger Bill Hooker said...

Further attractive features for funders include increased research impact and efficiency. Just as there is a large and steadily growing body of evidence that Open Access increases the citation frequencies of published work, so it can be inferred that Open Science will lead to increased visibility and usage of research data. Similarly, Open Access to preprints in the physics database arXiv has been shown to speed up the research cycle significantly. It would hardly be surprising if making the same information available even earlier in its production cycle (by means of Open Notebook Science) had a further salutary effect.

Mendeleev's law of periodicity was formulated by examination of data he himself did not produce. What Open Notebook Science aims to do is to put tools and information in the hands of tomorrow's Mendeleevs.

At 10:59 AM, Blogger Jean-Claude Bradley said...

I really appreciate your support. The more we talk about it the more people we can get involved.


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